feat: Add simplerspec_to_hyperSpec

NAMESPACE

@@ -4,5 +4,6 @@ export(ChemoSpec_to_hyperSpec)
 export(hyperSpec_to_ChemoSpec)
 export(matrix_to_ChemoSpec)
 export(simplerspec_to_ChemoSpec)
+export(simplerspec_to_hyperSpec)
 export(to_ChemoSpec)
 export(to_hyperSpec)

R/to_hyperSpec.R

@@ -67,3 +67,84 @@ ChemoSpec_to_hyperSpec <- function(Spectra, ...) {
     ...
   )
 }
+
+#' {simplerspec} ⚪ ➡️ 🔵 {hyperSpec}
+#'
+#' Some data will not be converted:
+#' - Spectra columns except the `spc_column`
+#' - Wavenumber columns except the `wavelength_column`
+#'
+#' @param spc_tbl [`simplerspec::gather_spc`],
+#'        [`simplerspec::resample_spc`], [`simplerspec::average_spc`],
+#'        or [`simplerspec::preprocess_spc`] spectra tibble.
+#' @param spc_column Column name of the data to use.
+#'        Must be one of `"spc_pre", "spc_mean", "spc_rs", "spc"`, or
+#'        any column name if `strict_column_check` is set to FALSE.
+#' @param wavelength_column Column name of the data to use.
+#'        Must be one of `"xvalues_pre", "wavenumbers_rs", "wavenumbers"`, or
+#'        any column name if `strict_column_check` is set to FALSE.
+#' @param unit_wavelength,unit_spc **Optional** labels for the x- and y-axis.
+#' @param .strict_column_check (**Default**: TRUE) Set this to FALSE to allow
+#'        using any valid column name on `spc_tbl` in `spc_column` and
+#'        `wavelength_column`.
+#' @inheritParams to_hyperSpec
+#' @inheritDotParams hyperSpec::new_hyperSpec gc
+#'
+#' @returns A `ChemoSpec::Spectra()` object.
+#'
+#' @examples
+#' data("simplerspec_opus")
+#' spectra <- simplerspec_to_hyperSpec(simplerspec_opus) |> str()
+#'
+#' @export
+#' @keywords from_simplerspec to_hyperSpec
+#' @seealso `to_hyperSpec()`, `simplerspec_to_ChemoSpec()`
+simplerspec_to_hyperSpec <- function(
+    spc_tbl,
+    spc_column = base::c("spc_pre", "spc_mean", "spc_rs", "spc"),
+    wavelength_column = base::c("xvalues_pre", "wavenumbers_rs", "wavenumbers"),
+    unit_spc = "{missing spectra unit}",
+    unit_wavelength = "{missing wavelength unit}",
+    .strict_column_check = TRUE,
+    ...) {
+  rlang::check_installed("tibble")
+
+  spc_tbl <- tibble::as_tibble(spc_tbl)
+
+  checkmate::assert_class(spc_tbl, base::c("tbl_df", "tbl", "data.frame"))
+
+  if (.strict_column_check) {
+    spc_column <- base::match.arg(spc_column, c("spc_pre", "spc_mean", "spc_rs", "spc"))
+    wavelength_column <- base::match.arg(wavelength_column, c("xvalues_pre", "wavenumbers_rs", "wavenumbers"))
+  } else {
+    spc_column <- base::match.arg(spc_column, colnames(spc_tbl))
+    wavelength_column <- base::match.arg(wavelength_column, colnames(spc_tbl))
+  }
+
+  spc <- base::do.call(rbind, spc_tbl[, spc_column][[1]]) |> as.matrix()
+  data <- base::do.call(rbind, spc_tbl$metadata) |> base::as.data.frame()
+  wavelength <- spc_tbl[, wavelength_column][[1]][[1]]
+
+  labels <- base::list(
+    .wavelength = unit_wavelength,
+    spc = unit_spc
+  )
+
+  for (data_name in colnames(data)) {
+    labels[[data_name]] <- data_name
+  }
+
+  # Because simplerspec contains a metadata field beginning with "spc"
+  # (spc_in_file), the check in hyperSpec for is.null(data$spc) will
+  # return that metadata column instead of NULL.
+  # To avoid causing an unnecessary warning message for package users,
+  # the spectra data is instead passed as part of data.
+  data$spc <- spc
+
+  to_hyperSpec(
+    data = data,
+    wavelength = wavelength,
+    labels = labels # ,
+    # ...
+  )
+}

man/simplerspec_to_hyperSpec.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/to_hyperSpec.R
+\name{simplerspec_to_hyperSpec}
+\alias{simplerspec_to_hyperSpec}
+\title{{simplerspec} ⚪ ➡️ 🔵 {hyperSpec}}
+\usage{
+simplerspec_to_hyperSpec(
+  spc_tbl,
+  spc_column = base::c("spc_pre", "spc_mean", "spc_rs", "spc"),
+  wavelength_column = base::c("xvalues_pre", "wavenumbers_rs", "wavenumbers"),
+  unit_spc = "{missing spectra unit}",
+  unit_wavelength = "{missing wavelength unit}",
+  .strict_column_check = TRUE,
+  ...
+)
+}
+\arguments{
+\item{spc_tbl}{\code{\link[simplerspec:gather_spc]{simplerspec::gather_spc}},
+\code{\link[simplerspec:resample_spc]{simplerspec::resample_spc}}, \code{\link[simplerspec:average_spc]{simplerspec::average_spc}},
+or \code{\link[simplerspec:preprocess_spc]{simplerspec::preprocess_spc}} spectra tibble.}
+
+\item{spc_column}{Column name of the data to use.
+Must be one of \verb{"spc_pre", "spc_mean", "spc_rs", "spc"}, or
+any column name if \code{strict_column_check} is set to FALSE.}
+
+\item{wavelength_column}{Column name of the data to use.
+Must be one of \verb{"xvalues_pre", "wavenumbers_rs", "wavenumbers"}, or
+any column name if \code{strict_column_check} is set to FALSE.}
+
+\item{unit_wavelength, unit_spc}{\strong{Optional} labels for the x- and y-axis.}
+
+\item{.strict_column_check}{(\strong{Default}: TRUE) Set this to FALSE to allow
+using any valid column name on \code{spc_tbl} in \code{spc_column} and
+\code{wavelength_column}.}
+
+\item{...}{
+  Arguments passed on to \code{\link[hyperSpec:initialize]{hyperSpec::new_hyperSpec}}
+  \describe{
+    \item{\code{gc}}{(logical) \cr Use garbage collection.
+If option \code{gc} is \code{TRUE}, the initialization will have frequent calls
+to \code{\link[base:gc]{base::gc()}}, which can help to avoid swapping or running out of
+memory. The default value of \code{gc} can be set via \code{\link[hyperSpec:hy_set_options]{hy_set_options()}}.}
+  }}
+}
+\value{
+A \code{ChemoSpec::Spectra()} object.
+}
+\description{
+Some data will not be converted:
+\itemize{
+\item Spectra columns except the \code{spc_column}
+\item Wavenumber columns except the \code{wavelength_column}
+}
+}
+\examples{
+data("simplerspec_opus")
+spectra <- simplerspec_to_hyperSpec(simplerspec_opus) |> str()
+
+}
+\seealso{
+\code{to_hyperSpec()}, \code{simplerspec_to_ChemoSpec()}
+}
+\keyword{from_simplerspec}
+\keyword{to_hyperSpec}

tests/testthat/test-simplerspec_to_hyperSpec.R

+test_that("simplerspec ➡️ hyperSpec: opus", {
+  skip_if_not_installed("simplerspec")
+  skip_if_not_installed("tibble")
+  skip_if_not_installed("hyperSpec")
+
+  data(simplerspec_opus)
+
+  skip_if_not(exists("simplerspec_opus"), "Example data set required for test")
+
+  hy <- simplerspec_to_hyperSpec(simplerspec_opus)
+
+  expect_s4_class(hy, "hyperSpec")
+})